The vault particle is enclosed by a C13-symmetric cap with a positively charged exterior

Vaults are some of the largest ribonucleoprotein complexes known and are highly conserved across eukaryotes, but both their function and key details of their architecture remain unclear. While high-resolution structures of the vault shell are available, the architecture and symmetry of the cap have remained unresolved. Here, we present a 2.25-angstrom cryo-electron microscopy structure of the vault cap, revealing an unexpected 13-fold symmetric arrangement that contrasts with the 39-fold symmetry of the vault body, with each repeating module of the cap formed by an asymmetric homotrimer of adjacent subunits. The center of the cap features an unusual architecture, consisting of two concentric β barrels surrounded by an interwoven two-layer stack of α helices. The vault cap features a positively charged exterior and a negatively charged interior surface, with implications for binding partner recruitment and engineering of modified vault particles.